Add option to list run-compatible pathogen repos

[victorlin]

Note

Requires server changes in nextstrain/nextstrain.org#1307

Description of proposed changes

This relies on a properly structured response from the /pathogen-repos endpoint.

Related issue(s)

Closes #502

Checklist

• Checks pass
• Update changelog

[victorlin]

Testing locally with the review app from nextstrain/nextstrain.org#1307:

$ NEXTSTRAIN_DOT_ORG=https://nextstrain-s-victorlin--evz0br.herokuapp.com nextstrain setup --list
Fetching available pathogens…

measles
  Workflows compatible with nextstrain run:
    - ingest
    - phylogenetic
    - nextclade
mumps
  Workflows compatible with nextstrain run:
    - ingest
    - phylogenetic
    - nextclade
ncov-ingest
  Workflows compatible with nextstrain run:
    - manual-upload
nipah
  Workflows compatible with nextstrain run:
    - ingest
    - phylogenetic
zika
  Workflows compatible with nextstrain run:
    - ingest
    - phylogenetic

[jameshadfield]

This is really nice. Having docs for each workflow (e.g. a GitHub link to the README) seems like a critical part of this from essentially day one, otherwise you install the pathogen... and then what?

Is there an existing command which shows me my currently installed pathogens and the available workflows? (without me looking in ~/.nextstrain/pathogens/!) If it doesn't exist then it would be a great thing to have. This may influence your choice of argument name here.

[victorlin]

@jameshadfield those are great ideas worth pursuing. We should first discuss the overall design. I've started a Google Doc for easier collaboration: Pathogen repo usage flow

[victorlin]

Some good design discussions are happening in the Google Doc, which will influence the implementation here. Marking as draft in the meantime.